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Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Journal of Integrative Plant Biology 2024年第4期66卷 824-843页

作者： Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo Cairong Zhong Suhua Shi ziwen he State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine School of Life SciencesFudan UniversityGuangzhou 511462China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms.here,we present a chromosome-level genome sequence and assembly for N.fruticans.We integrated the genomes of N.fruticans and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this clade.We also inferred a low mutation rate for the N.fruticans genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary period.Moreover,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in N.fruticans.Furthermore,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in N.fruticans underly its crypto-vivipary characteristics,reflecting its intertidal adaptation.Our study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove palm.Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关键词： crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans palm

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Distributed Source-Load-Storage Cooperative Low-Carbon Scheduling Strategy Considering Vehicle-to-Grid Aggregators

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Journal of Modern Power Systems and Clean Energy 2024年第2期12卷 440-453页

作者： Xiao Xu ziwen Qiu Teng Zhang Hui Gao School of Automation Nanjing University of Posts and TelecommunicationsNanjing210023China

The vehicle-to-grid(V2G)technology enables the bidirectional power flow between electric vehicle(EV)batteries and the power grid,making EV-based mobile energy storage an appealing supplement to stationary energy storage systems.However,the stochastic and volatile charging behaviors pose a challenge for EV fleets to engage directly in multi-agent cooperation.To unlock the scheduling potential of EVs,this paper proposes a source-load-storage cooperative low-carbon scheduling strategy considering V2G aggregators.The uncertainty of EV charging patterns is managed through a rolling-horizon control framework,where the scheduling and control horizons are adaptively adjusted according to the availability periods of EVs.Moreover,a Minkowski-sum based aggregation method is employed to evaluate the scheduling potential of aggregated EV fleets within a given scheduling horizon.This method effectively reduces the variable dimension while preserving the charging and discharging constraints of individual EVs.Subsequently,a Nash bargaining based cooperative scheduling model involving a distribution system operator(DSO),an EV aggregator(EVA),and a load aggregator(LA)is established to maximize the social welfare and improve the low-carbon performance of the system.This model is solved by the alternating direction method of multipliers(ADMM)algorithm in a distributed manner,with privacy of participants fully preserved.The proposed strategy is proven to achieve the objective of low-carbon economic operation.

关键词： Electric vehicle(EV) low-carbon scheduling mobile storage system Nash bargaining power flexibility alternating direction method of multipliers(ADMM).

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Unveiling the mechanisms of Fe(Ⅲ)-loaded chitosan composite(CTS-Fe)in enhancing anaerobic digestion of waste activated sludge

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Journal of Environmental Sciences 2024年第4期138卷 200-211页

作者： Boaiqi Zhang ziwen Zhao RuiMa Nan Chen Zhe Kong Zhongfang Lei Zhenya Zhang Graduate School of Life and Environmental Sciences University of Tsukuba1-1-1 TennodaiTsukubaIbaraki 305-8572Japan The Key Laboratory of Water and Sediment Sciences Ministry of Education/State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems/College of Environmental Sciences and EngineeringPeking UniversityBeijing 100871China South China Institute of Environmental Sciences Ministry of Ecology and EnvironmentGuangzhou 510345China School of Water Resources and Environment China University of Geosciences(Beijing)Beijing 100083China School of Environmental Science and Engineering Suzhou University of Science and TechnologySuzhou 215009China

Anaerobic digestion(AD)of waste activated sludge(WAS)is usually limited by the low generation efficiency of methane.Fe(Ⅲ)-loaded chitosan composite(CTS-Fe)have been reported to effectively enhanced the digestion of WAS,but its role in promoting anaerobic sludge digestion remains unclear.In present study,the effects of CTS-Fe on the hydrolysis and methanogenesis stages of WAS anaerobic digestion were investigated.The addition of CTSFe increased methane production potential by 8%-23%under the tested conditions with the addition of 5-20 g/L CTS-Fe.Besides,the results demonstrate that the addition of CTS-Fe could effectively promote the hydrolysis of WAS,evidenced by lower protein or polysaccharides concentration,higher soluble organic carbon in rector adding CTS-Fe,as well as the increased activity of extracellular hydrolase with higher CTS-Fe concentration.Meanwhile,the enrichment of Clostridia abundance(iron-reducing bacteria(IRBs))was observed in CTS-Fe adding reactor(8.9%-13.8%),which was higher than that in the control reactor(7.9%).The observation further suggesting the acceleration of hydrolysis through dissimilatory iron reduction(DIR)process,thus providing abundant substrates for methanogenesis.However,the presence of CTS-Fe was inhibited the acetoclastic and hydrogenotrophic methanogenesis process,which could be ascribed to the Fe(Ⅲ)act as electron acceptor coupled to methane for anaerobic oxidation.Furthermore,coenzyme F420 activity in the CTS-Fe added reactor was 34.9% lower than in the blank,also abundance of microorganisms involved in hydrogenotrophic methanogenesis was decreased.Results from this study could provide theoretical support for the practical applications of CTS-Fe.

关键词： Chitosan-Fe(Ⅲ)composite Methanogenesis Dissimilatory iron reduction Enzyme activity Microbial community structure

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Two decades of suspect evidence for adaptive molecular evolution——negative selection confounding positive-selection signals

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National Science Review 2022年第5期9卷 129-141页

作者： Qipian Chen Hao Yang Xiao Feng Qingjian Chen Suhua Shi Chung-Ⅰ Wu ziwen he State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-sen University

There has been a large literature in the last two decades affirming adaptive DNA sequence evolution between species.The main lines of evidence are from(i) the McDonald-Kreitman(MK) test,which compares divergence and polymorphism data,and(ii) the phylogenetic analysis by maximum likelihood(PAML) test,which analyzes multispecies divergence data.here,we apply these two tests concurrently to genomic data of Drosophila and Arabidopsis.To our surprise,the> 100 genes identified by the two tests do not overlap beyond random expectation.Because the non-concordance could be due to low powers leading to high false negatives,we merge every 20-30 genes into a ’supergene’.At the supergene level,the power of detection is large but the calls still do not overlap.We rule out methodological reasons for the non-concordance.In particular,extensive simulations fail to find scenarios whereby positive selection can only be detected by either MK or PAML,but not both.Since molecular evolution is governed by positive and negative selection concurrently,a fundamental assumption for estimating one of these(say,positive selection) is that the other is constant.However,in a broad survey of primates,birds,Drosophila and Arabidopsis,we found that negative selection rarely stays constant for long in evolution.As a consequence,the variation in negative selection is often misconstrued as a signal of positive selection.In conclusion,MK,PAML and any method that examines genomic sequence evolution has to explicitly address the variation in negative selection before estimating positive selection.In a companion study,we propose a possible path forward in two stages—first,by mapping out the changes in negative selection and then using this map to estimate positive selection.For now,the large literature on positive selection between species has to await reassessment.

关键词： molecular evolution neutral theory natural selection

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The twin-beginnings of COVID-19 in Asia and Europe—one prevails quickly

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National Science Review 2022年第4期9卷 51-59页

作者： Yongsen Ruan Haijun Wen Mei Hou ziwen he Xuemei Lu Yongbiao Xue Xionglei he Ya-Ping Zhang Chung-I Wu State Key Laboratory of Biocontrol School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Sun Yat-sen University Department of Ecology and Evolution University of Chicago State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Beijing Institute of Genomics Chinese Academy of Sciencesand China National Centre for Bioinformation

In the spread of SARS-C oV-2,there have been multiple waves of replacement between strains,each of which having a distinct set of mutations.The first wave is a group of four mutations(C241 T,C3037 T,C14408 T and A23403 G [this being the amino acid change D614 G];all designated 0 to 1 below).This DG(D614 G) group,fixed at the start of the pandemic,is the foundation of all subsequent waves of strains.Curiously,the DG group is absent in early Asian samples but present(and likely common) in Europe from the beginning.European data show that the high fitness of DG1111 requires the synergistic effect of all four mutations.However,the European strains would have had no time to evolve the four DG mutations(0 to1),had they come directly from the early Asian DG0000 strain.Very likely,the European DG1111 strain had acquired the highly adaptive DG mutations in pre-pandemic Europe and had been spreading in parallel with the Asian strains.Two recent reports further support this twin-beginning interpretation.There was a period of two-way spread between Asia and Europe but,by May 2020,the European strains had supplanted the Asian strains globally.This large-scale replacement of one set of mutations for another has since been replayed many times as COVID-19 progresses.

关键词： COVID-19 D614G SARS-CoV-2 fitness advantage twin-beginnings

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Supported Atomically Dispersed Pd Catalyzed Direct Alkoxylation and Allylic Alkylation

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Chinese Journal of Chemistry 2024年第7期42卷 719-724页

作者： Ruixuan Qin ziwen Chen Qingyuan Wu Nanfeng Zheng Pengxin Liu New Cornerstone Science Laboratory State Key Laboratory for Physical Chemistry of Solid SurfacesCollaborative Innovation Center of Chemistry for Energy Materialsand National&Local Joint Engineering Research Center of Preparation Technology of NanomaterialsCollege of Chemistry and Chemical EngineeringXiamen UniversityXiamenFujian 361005China Innovation Laboratry for Scences and Technoogies of Energy Materials of Fujan Province(IKKM) Xiamen Fujian 361102China School of Physical Science and Technology Shanghai Tech UniversityShanghai 201210China Fujian Key Laboratory of Rare-earth Functional Materials Fujian Shanhai Collaborative Innovation Center of Rare-earth Functional MaterialsLongyanFujian 366300China

A new approach to allylic alkylation is realized using an atomically dispersed palladium catalyst(Pd1/TiO2-EG).Unlike conventional methods that require derivation of substrates and utilization of additives,this method allows for direct allylic alkylation from allylic alcohols,producing H2O as the sole by-product.The catalyst's high efficiency is attributed to the local hydrogen bonding at the or-ganic-inorganic interface(Pd-EG interface),facilitating hydroxyl group activation forη3π-allyl complex formation.The system demonstrates successful direct C—O and C—C coupling reactions with high selectivity,requiring no additives.This study highlights the potential of supported atomically dispersed catalysts for greener and more efficient catalysis,meanwhile,offers unique insights into the distinct behavior of atomically dispersed catalysts in comparison to homogeneous or nanoparticle-based catalysts.

关键词： Atomically dispersed catalyst Alkylation C—C coupling Organic-inorganic Interface Hydrogen bond Tsuji-Trost reaction Green catalysis

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Adaptive convergence at the genomic level——prevalent, uncommon or very rare?

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National Science Review 2020年第6期7卷 947-951页

作者： ziwen he Shaohua Xu Suhua Shi School of Life Sciences Sun Yat-sen University

Convergent evolution is one of the central topics in evolutionary genetics [1].While there has been ample evidence of phenotypic convergence, the issue is whether each and any of the phenotypic convergences have an underlying cause in genic convergence [2,3]. Fortunately,the torrent of genomic data has made it possible to address the issue [4–8].Convergence can happen at multiple

关键词： EVOLUTION ADAPTATION

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Towards Lessening Learners’Aversive Emotions and Promoting Their Mental health:Developing and Validating a Measurement of English Speaking Demotivation in the Chinese EFL Context

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International Journal of Mental health Promotion 2024年第2期26卷 161-175页

作者： Chili Li Xinxin Zhao ziwen Pan Ting Yi Long Qian School of Foreign Languages Hubei University of TechnologyWuhan430068China Faculty of Education The University of Hong KongHong Kong999077China School of Foreign Languages Henan UniversityKaifeng450046China Research Institute of International Chinese Language Education Beijing Language and Culture UniversityBeijing100083China Faculty of Humanities The Hong Kong Polytechnic UniversityHong Kong100872China School of Humanities Wuhan University of Engineering ScienceWuhan430200China

While a plethora of studies has been conducted to explore demotivation and its impact on mental health in second language(L2)education,scanty research focuses on demotivation in L2 speaking learning.Particularly,little research explores the measures to quantify L2 speaking demotivation.The present two-phase study attempts to develop and validate an English Speaking Demotivation Scale(ESDS).To this end,an independent sample of 207 Chinese tertiary learners of English as a Foreign Language(EFL)participated in the development phase,and another group of 188 Chinese EFL learners was recruited for the validation of the scale.Exploratory Factor Analysis(EFA)and Confirmatory Factor Analysis(CFA)were employed to determine the factor structure of the scale.The EFA results revealed a six-factor solution with Teacher-related Factors in Learning Spoken English(TFLSE),Interest and Valence in Learning Spoken English(IVLSE),Self-efficacy in Learning Spoken English(SELSE),Negative Peer Influence in Learning Spoken English(NPILSE),Undesirable Environment for Learning Spoken English(UELSE),and Negative Influence of Assessment and Learning Materials in speaking class(NIALM).In the validation phase,Confirmatory Factor Analysis(CFA)was performed to validate the internal structure of the scale.The CFA results showed that the model fits the data well.Overall,the ESDS is a robust and trustworthy psychometric tool that could be utilized to examine L2 speaking demotivation.Implications for diminishing EFL learners’demotivation,lessening their aversive emotions and promoting their mental health are also discussed.

关键词： Demotivation for learning English speaking ESDS scale development and validation Chinese EFL learners mental health

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Extensive gene flow in secondary sympatry after allopatric speciation

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National Science Review 2022年第12期9卷 24-36页

作者： Xinfeng Wang ziwen he Zixiao Guo Ming Yang Shaohua Xu Qipian Chen Shao Shao Sen Li Cairong Zhong Norman C.Duke Suhua Shi State Key Laboratory of Biocontrol Guangdong Key Laboratory of Plant Resources School of Life SciencesSouthern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Sun Yat-sen University Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Department of Laboratory Medicine& Pathology University of Washington Hainan Academy of Forestry (Hainan Academy of Mangrove) Centre for Tropical Water and Aquatic Ecosystem Research James Cook University

In the conventional view,species are separate gene pools delineated by reproductive isolation(RI).In an alternative view,species may also be delineated by a small set of ’speciation genes’ without full RI,a view that has gained broad acceptance.A recent survey,however,suggested that the extensive literature on’speciation with gene flow’ is mostly(if not all) about exchanges in the early stages of speciation.There is no definitive evidence that the observed gene flow actually happened after speciation is completed.here,we wish to know whether ’good species’(defined by the ’secondary sympatry’ test) do continue to exchange genes and,importantly,under what conditions such exchanges can be observed.De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species(Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry.They became sympatric in northeastern Australia but remain distinct species.Nevertheless,their genomes harbor～4000-10 000 introgression blocks averaging only about 3-4 Kb.These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable ’genomic islets,’～1.4 Kb in size,often harbor diverging genes of flower or gamete development.The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs.micro-allopatric speciation.In conclusion,true’good species’ may often continue to exchange genes but the opportunity for detection is highly constrained.

关键词： mangroves population genomics speciation introgression species hybridization

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Sympatric or micro-allopatric speciation in a glacial lake?Genomic islands support neither

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National Science Review 2022年第12期9卷 37-49页

作者： Ning Sun Liandong Yang Fei Tian Honghui Zeng ziwen he Kai Zhao Cheng Wang Minghui Meng Chenguang Feng Chengchi Fang Wenqi Lv Jing Bo Yongtao Tang Xiaoni Gan Zuogang Peng Yiyu Chen Shunping he State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources School of Life Sciences Sun Yat-sen University School of Ecology and Environment Northwestern Polytechnical University Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences National Natural Science Foundation of China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation.One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence,wherein divergent DNA segments are interspersed with low-divergence segments.Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.Sympatric divergence of endemic fishes is known from isolated saline,crater,postglacial,and ancient lakes.Two morphologically distinct cyprinid fishes,Gymnocypris eckloni scoliostomus(GS) and G.eckloni eckloni(GE),in a small glacial lake on the Qinghai-Tibet Plateau,Lake Sunmcuo,match the biogeographic criteria of sympatric speciation.In this study,we examined genome-wide variation in 46individuals from these two groups.The divergence time between the GS and GE lineages was estimated to be 20-60 Kya.We identified 54 large genomic islands(≥100 kb) of speciation,which accounted for 89.4%of the total length of all genomic islands.These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes.Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation,they were too large to support the hypothesis of sympatric speciation.Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands(as small as a few kilobases in size).Thus,the observed pattern is consistent with the extensive evidence on parapatric speciation,in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation.We suggest that many,if not most,of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

关键词： sympatric speciation gene flow genomic islands micro-parapatric speciation selection olfaction

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